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Honghan Wu edited this page Nov 16, 2017 · 21 revisions

Welcome to the SemEHR wiki!

Run SemEHR pipeline

A typical SemEHR process contains the following steps:

  • query a database to get the documents for processing
  • NLP processing (e.g., using bio-yodie to annotate umls concepts)
  • index contextualised concepts into an elaticsearch instance
  • do patient centric indexing to integrate all patient docs and annotations

To do the process, the easiest way is to

  1. edit the process configuration file using the template in index_settings/semehr_process_settings.json.
  2. run the script python semehr_processor.py PATH_TO_YOUR_CONFIGURATION

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